Starting phenix.real_space_refine on Mon Aug 25 04:46:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjs_50511/08_2025/9fjs_50511.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjs_50511/08_2025/9fjs_50511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjs_50511/08_2025/9fjs_50511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjs_50511/08_2025/9fjs_50511.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjs_50511/08_2025/9fjs_50511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjs_50511/08_2025/9fjs_50511.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 10 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 15884 2.51 5 N 4527 2.21 5 O 4896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25413 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "b" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1759 Classifications: {'peptide': 231} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 8742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8742 Classifications: {'peptide': 1126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1063} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 9951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9951 Classifications: {'peptide': 1269} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1208} Chain breaks: 1 Chain: "e" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 75} Chain: "f" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain: "O" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19281 SG CYS d 891 109.639 65.943 85.057 1.00 36.05 S ATOM 19855 SG CYS d 968 106.129 65.213 86.454 1.00 35.82 S ATOM 19897 SG CYS d 975 106.638 67.206 83.180 1.00 29.13 S ATOM 19915 SG CYS d 978 107.306 63.599 83.185 1.00 31.31 S ATOM 12701 SG CYS d 60 69.609 107.202 117.948 1.00 76.12 S ATOM 12719 SG CYS d 62 66.723 109.116 119.507 1.00 85.46 S ATOM 12828 SG CYS d 75 70.374 109.210 120.930 1.00 83.03 S ATOM 12854 SG CYS d 78 68.061 106.169 121.325 1.00 77.95 S Time building chain proxies: 5.18, per 1000 atoms: 0.20 Number of scatterers: 25413 At special positions: 0 Unit cell: (131.024, 144.816, 199.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 93 16.00 P 10 15.00 Mg 1 11.99 O 4896 8.00 N 4527 7.00 C 15884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d1501 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 975 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 978 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 891 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 968 " pdb=" ZN d1502 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 60 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 78 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 62 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 75 " Number of angles added : 12 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5946 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 43 sheets defined 43.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'a' and resid 30 through 43 Processing helix chain 'a' and resid 72 through 82 removed outlier: 3.984A pdb=" N SER a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 110 No H-bonds generated for 'chain 'a' and resid 108 through 110' Processing helix chain 'a' and resid 148 through 153 Processing helix chain 'a' and resid 203 through 225 removed outlier: 4.137A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 46 removed outlier: 4.010A pdb=" N THR b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 82 Processing helix chain 'b' and resid 108 through 110 No H-bonds generated for 'chain 'b' and resid 108 through 110' Processing helix chain 'b' and resid 203 through 225 removed outlier: 3.813A pdb=" N LEU b 221 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU b 225 " --> pdb=" O LEU b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 65 removed outlier: 4.096A pdb=" N SER c 60 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE c 61 " --> pdb=" O GLN c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 78 removed outlier: 3.638A pdb=" N GLU c 76 " --> pdb=" O GLU c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 93 removed outlier: 3.826A pdb=" N TYR c 91 " --> pdb=" O GLU c 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 125 Processing helix chain 'c' and resid 226 through 229 Processing helix chain 'c' and resid 234 through 241 Processing helix chain 'c' and resid 244 through 252 Processing helix chain 'c' and resid 255 through 265 Processing helix chain 'c' and resid 269 through 282 Processing helix chain 'c' and resid 288 through 301 Processing helix chain 'c' and resid 309 through 321 Processing helix chain 'c' and resid 334 through 351 Processing helix chain 'c' and resid 380 through 407 Processing helix chain 'c' and resid 413 through 418 Processing helix chain 'c' and resid 420 through 434 Processing helix chain 'c' and resid 444 through 453 Processing helix chain 'c' and resid 469 through 474 removed outlier: 3.893A pdb=" N ARG c 473 " --> pdb=" O GLY c 469 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP c 474 " --> pdb=" O LEU c 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 469 through 474' Processing helix chain 'c' and resid 532 through 539 removed outlier: 4.054A pdb=" N ARG c 538 " --> pdb=" O ASP c 534 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS c 539 " --> pdb=" O GLU c 535 " (cutoff:3.500A) Processing helix chain 'c' and resid 582 through 587 removed outlier: 4.459A pdb=" N MET c 586 " --> pdb=" O PRO c 583 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL c 587 " --> pdb=" O ARG c 584 " (cutoff:3.500A) Processing helix chain 'c' and resid 590 through 594 removed outlier: 3.730A pdb=" N ILE c 594 " --> pdb=" O THR c 591 " (cutoff:3.500A) Processing helix chain 'c' and resid 596 through 600 Processing helix chain 'c' and resid 601 through 612 Processing helix chain 'c' and resid 629 through 638 removed outlier: 4.382A pdb=" N ARG c 633 " --> pdb=" O GLY c 629 " (cutoff:3.500A) Processing helix chain 'c' and resid 739 through 744 Processing helix chain 'c' and resid 815 through 826 Processing helix chain 'c' and resid 856 through 858 No H-bonds generated for 'chain 'c' and resid 856 through 858' Processing helix chain 'c' and resid 900 through 904 Processing helix chain 'c' and resid 920 through 926 removed outlier: 4.263A pdb=" N ARG c 924 " --> pdb=" O HIS c 920 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG c 925 " --> pdb=" O GLY c 921 " (cutoff:3.500A) Processing helix chain 'c' and resid 928 through 943 Processing helix chain 'c' and resid 953 through 957 Processing helix chain 'c' and resid 960 through 964 removed outlier: 3.916A pdb=" N LEU c 964 " --> pdb=" O ASP c 961 " (cutoff:3.500A) Processing helix chain 'c' and resid 981 through 990 removed outlier: 3.554A pdb=" N SER c 990 " --> pdb=" O GLN c 986 " (cutoff:3.500A) Processing helix chain 'c' and resid 1069 through 1080 Processing helix chain 'c' and resid 1081 through 1090 removed outlier: 3.727A pdb=" N LEU c1085 " --> pdb=" O ALA c1081 " (cutoff:3.500A) Processing helix chain 'c' and resid 1095 through 1108 Processing helix chain 'c' and resid 1118 through 1129 Processing helix chain 'd' and resid 16 through 24 Processing helix chain 'd' and resid 84 through 90 Processing helix chain 'd' and resid 112 through 119 Processing helix chain 'd' and resid 121 through 130 Processing helix chain 'd' and resid 140 through 147 Processing helix chain 'd' and resid 147 through 187 Processing helix chain 'd' and resid 191 through 229 Processing helix chain 'd' and resid 237 through 248 Processing helix chain 'd' and resid 257 through 268 Processing helix chain 'd' and resid 270 through 283 removed outlier: 3.528A pdb=" N ASN d 283 " --> pdb=" O ASP d 279 " (cutoff:3.500A) Processing helix chain 'd' and resid 285 through 304 Processing helix chain 'd' and resid 308 through 311 removed outlier: 3.550A pdb=" N GLY d 311 " --> pdb=" O SER d 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 308 through 311' Processing helix chain 'd' and resid 321 through 325 Processing helix chain 'd' and resid 338 through 361 removed outlier: 4.033A pdb=" N ASP d 342 " --> pdb=" O SER d 338 " (cutoff:3.500A) Processing helix chain 'd' and resid 363 through 383 Processing helix chain 'd' and resid 401 through 406 removed outlier: 3.502A pdb=" N LEU d 405 " --> pdb=" O LEU d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 411 through 419 Processing helix chain 'd' and resid 445 through 452 removed outlier: 3.637A pdb=" N LEU d 449 " --> pdb=" O LYS d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 452 through 463 Processing helix chain 'd' and resid 468 through 479 Processing helix chain 'd' and resid 481 through 491 removed outlier: 4.301A pdb=" N ASP d 485 " --> pdb=" O PRO d 481 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL d 486 " --> pdb=" O GLN d 482 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU d 489 " --> pdb=" O ASP d 485 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE d 491 " --> pdb=" O LEU d 487 " (cutoff:3.500A) Processing helix chain 'd' and resid 505 through 507 No H-bonds generated for 'chain 'd' and resid 505 through 507' Processing helix chain 'd' and resid 528 through 533 Processing helix chain 'd' and resid 548 through 558 Processing helix chain 'd' and resid 560 through 564 Processing helix chain 'd' and resid 580 through 590 Processing helix chain 'd' and resid 614 through 625 Processing helix chain 'd' and resid 643 through 651 removed outlier: 3.787A pdb=" N GLU d 649 " --> pdb=" O GLU d 645 " (cutoff:3.500A) Processing helix chain 'd' and resid 668 through 675 Processing helix chain 'd' and resid 689 through 702 Processing helix chain 'd' and resid 705 through 726 removed outlier: 3.666A pdb=" N THR d 725 " --> pdb=" O PHE d 721 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG d 726 " --> pdb=" O TYR d 722 " (cutoff:3.500A) Processing helix chain 'd' and resid 742 through 762 Processing helix chain 'd' and resid 766 through 793 Processing helix chain 'd' and resid 797 through 805 removed outlier: 3.882A pdb=" N VAL d 803 " --> pdb=" O ILE d 799 " (cutoff:3.500A) Processing helix chain 'd' and resid 810 through 817 removed outlier: 3.602A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.013A pdb=" N HIS d 854 " --> pdb=" O PHE d 850 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY d 855 " --> pdb=" O ILE d 851 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA d 856 " --> pdb=" O ASN d 852 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA d 864 " --> pdb=" O LEU d 860 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU d 865 " --> pdb=" O ALA d 861 " (cutoff:3.500A) Processing helix chain 'd' and resid 945 through 956 Processing helix chain 'd' and resid 964 through 968 Processing helix chain 'd' and resid 976 through 980 Processing helix chain 'd' and resid 994 through 1005 removed outlier: 3.699A pdb=" N VAL d 998 " --> pdb=" O ALA d 994 " (cutoff:3.500A) Processing helix chain 'd' and resid 1006 through 1009 Processing helix chain 'd' and resid 1027 through 1037 removed outlier: 3.535A pdb=" N VAL d1031 " --> pdb=" O GLY d1027 " (cutoff:3.500A) Processing helix chain 'd' and resid 1117 through 1125 Processing helix chain 'd' and resid 1126 through 1145 removed outlier: 3.520A pdb=" N VAL d1130 " --> pdb=" O GLY d1126 " (cutoff:3.500A) Processing helix chain 'd' and resid 1151 through 1163 removed outlier: 4.499A pdb=" N ILE d1157 " --> pdb=" O HIS d1153 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN d1160 " --> pdb=" O VAL d1156 " (cutoff:3.500A) Processing helix chain 'd' and resid 1182 through 1197 removed outlier: 4.041A pdb=" N ALA d1188 " --> pdb=" O ALA d1184 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU d1189 " --> pdb=" O GLU d1185 " (cutoff:3.500A) Processing helix chain 'd' and resid 1211 through 1218 removed outlier: 3.647A pdb=" N THR d1217 " --> pdb=" O ALA d1213 " (cutoff:3.500A) Processing helix chain 'd' and resid 1219 through 1225 removed outlier: 4.141A pdb=" N SER d1225 " --> pdb=" O LEU d1221 " (cutoff:3.500A) Processing helix chain 'd' and resid 1228 through 1240 Processing helix chain 'd' and resid 1247 through 1255 removed outlier: 3.612A pdb=" N ILE d1253 " --> pdb=" O LYS d1249 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE d1254 " --> pdb=" O GLU d1250 " (cutoff:3.500A) Processing helix chain 'd' and resid 1264 through 1269 removed outlier: 3.866A pdb=" N ASN d1269 " --> pdb=" O ASN d1265 " (cutoff:3.500A) Processing helix chain 'd' and resid 1275 through 1283 removed outlier: 3.628A pdb=" N TYR d1283 " --> pdb=" O ARG d1279 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 45 removed outlier: 3.791A pdb=" N LEU e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 71 removed outlier: 3.970A pdb=" N ILE e 55 " --> pdb=" O TYR e 51 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 101 Processing helix chain 'f' and resid 25 through 37 removed outlier: 4.187A pdb=" N THR f 37 " --> pdb=" O GLY f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 63 removed outlier: 4.140A pdb=" N GLU f 63 " --> pdb=" O GLU f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 103 removed outlier: 3.540A pdb=" N ARG f 74 " --> pdb=" O GLU f 70 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG f 96 " --> pdb=" O GLU f 92 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU f 97 " --> pdb=" O ALA f 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL f 98 " --> pdb=" O ASN f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 106 No H-bonds generated for 'chain 'f' and resid 104 through 106' Processing helix chain 'f' and resid 111 through 129 removed outlier: 3.562A pdb=" N LYS f 129 " --> pdb=" O ARG f 125 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 158 removed outlier: 3.791A pdb=" N TYR f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP f 144 " --> pdb=" O THR f 140 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP f 145 " --> pdb=" O TYR f 141 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 186 Processing helix chain 'f' and resid 190 through 199 Processing helix chain 'f' and resid 201 through 213 Processing helix chain 'f' and resid 229 through 234 removed outlier: 4.111A pdb=" N PHE f 233 " --> pdb=" O PRO f 229 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE f 234 " --> pdb=" O LEU f 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 229 through 234' Processing helix chain 'f' and resid 240 through 262 Processing helix chain 'f' and resid 263 through 275 Processing helix chain 'f' and resid 283 through 292 Processing helix chain 'f' and resid 296 through 310 removed outlier: 4.171A pdb=" N GLN f 300 " --> pdb=" O GLU f 296 " (cutoff:3.500A) Processing helix chain 'f' and resid 312 through 319 removed outlier: 3.633A pdb=" N ASP f 316 " --> pdb=" O GLY f 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 8 through 15 removed outlier: 3.633A pdb=" N GLU a 24 " --> pdb=" O THR a 8 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG a 18 " --> pdb=" O LEU a 14 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASP a 190 " --> pdb=" O PRO a 25 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS a 191 " --> pdb=" O VAL a 178 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL a 178 " --> pdb=" O LYS a 191 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE a 193 " --> pdb=" O TYR a 176 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR a 176 " --> pdb=" O ILE a 193 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP a 195 " --> pdb=" O VAL a 174 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL a 174 " --> pdb=" O ASP a 195 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU a 197 " --> pdb=" O LEU a 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 93 through 100 removed outlier: 7.468A pdb=" N GLU a 135 " --> pdb=" O ILE a 56 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE a 56 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU a 137 " --> pdb=" O ILE a 54 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE a 54 " --> pdb=" O GLU a 137 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL a 139 " --> pdb=" O THR a 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU a 141 " --> pdb=" O ALA a 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'a' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'a' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'b' and resid 8 through 10 removed outlier: 6.676A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 8 through 10 removed outlier: 6.676A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS b 173 " --> pdb=" O GLU b 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 93 through 100 removed outlier: 7.222A pdb=" N GLU b 135 " --> pdb=" O ILE b 56 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE b 56 " --> pdb=" O GLU b 135 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU b 137 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE b 54 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL b 139 " --> pdb=" O THR b 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 93 through 100 removed outlier: 3.566A pdb=" N VAL b 147 " --> pdb=" O SER b 166 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER b 166 " --> pdb=" O VAL b 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 85 through 86 Processing sheet with id=AB2, first strand: chain 'b' and resid 103 through 106 Processing sheet with id=AB3, first strand: chain 'c' and resid 39 through 40 removed outlier: 6.821A pdb=" N VAL c 39 " --> pdb=" O SER c 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'c' and resid 105 through 112 removed outlier: 6.898A pdb=" N PHE c 134 " --> pdb=" O PRO c 110 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE c 112 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY c 155 " --> pdb=" O LEU c 133 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL c 135 " --> pdb=" O PHE c 153 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE c 153 " --> pdb=" O VAL c 135 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA c 137 " --> pdb=" O THR c 151 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR c 151 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE c 139 " --> pdb=" O SER c 149 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N SER c 149 " --> pdb=" O PHE c 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'c' and resid 376 through 379 removed outlier: 3.851A pdb=" N SER c 177 " --> pdb=" O ARG c 454 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU c 455 " --> pdb=" O GLY c 498 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 184 through 191 removed outlier: 3.827A pdb=" N TYR c 186 " --> pdb=" O LYS c 203 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL c 202 " --> pdb=" O PHE c 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 354 through 356 Processing sheet with id=AB9, first strand: chain 'c' and resid 505 through 506 removed outlier: 3.935A pdb=" N LYS c 518 " --> pdb=" O GLU c 527 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU c 527 " --> pdb=" O LYS c 518 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'c' and resid 558 through 559 removed outlier: 3.559A pdb=" N VAL c 559 " --> pdb=" O VAL c 571 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL c 571 " --> pdb=" O VAL c 559 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'c' and resid 642 through 643 removed outlier: 6.791A pdb=" N VAL c 642 " --> pdb=" O ILE c 702 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS c 687 " --> pdb=" O ASP c 704 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 667 through 671 removed outlier: 3.597A pdb=" N ARG c 668 " --> pdb=" O VAL c 660 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR c 657 " --> pdb=" O VAL c 653 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL c 653 " --> pdb=" O TYR c 657 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR c 659 " --> pdb=" O GLU c 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 676 through 677 Processing sheet with id=AC6, first strand: chain 'c' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'c' and resid 1007 through 1008 removed outlier: 3.910A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU c 737 " --> pdb=" O GLY c 896 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE c 898 " --> pdb=" O LEU c 737 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE c 915 " --> pdb=" O ASN c 718 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU c 720 " --> pdb=" O ILE c 915 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU c 917 " --> pdb=" O LEU c 720 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA c 722 " --> pdb=" O LEU c 917 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE c 723 " --> pdb=" O THR c1024 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR c1024 " --> pdb=" O ILE c 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 749 through 760 removed outlier: 3.608A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY c 849 " --> pdb=" O TYR c 872 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA c 874 " --> pdb=" O VAL c 847 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'c' and resid 801 through 803 removed outlier: 6.803A pdb=" N LEU c 837 " --> pdb=" O LEU c 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 1066 through 1068 removed outlier: 3.588A pdb=" N GLN c1066 " --> pdb=" O VAL d 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS d 420 " --> pdb=" O PHE c1068 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 1133 through 1136 Processing sheet with id=AD4, first strand: chain 'd' and resid 73 through 74 removed outlier: 4.180A pdb=" N ILE d 73 " --> pdb=" O VAL d 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 93 through 102 removed outlier: 3.550A pdb=" N GLY d 93 " --> pdb=" O VAL d 319 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP d 315 " --> pdb=" O LEU d 97 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N ALA d 99 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N VAL d 313 " --> pdb=" O ALA d 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 134 through 135 Processing sheet with id=AD7, first strand: chain 'd' and resid 327 through 330 removed outlier: 3.806A pdb=" N ARG d 334 " --> pdb=" O LEU d 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 427 through 432 removed outlier: 7.710A pdb=" N ILE d 522 " --> pdb=" O ARG d 427 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL d 429 " --> pdb=" O ILE d 522 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU d 524 " --> pdb=" O VAL d 429 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 497 " --> pdb=" O HIS d 544 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER d 428 " --> pdb=" O MET d 541 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 611 through 612 removed outlier: 7.926A pdb=" N TYR d 612 " --> pdb=" O ARG d 636 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'd' and resid 898 through 900 removed outlier: 3.673A pdb=" N VAL d 960 " --> pdb=" O VAL d 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 902 through 904 removed outlier: 3.515A pdb=" N GLU d 903 " --> pdb=" O ILE d 911 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 1043 through 1044 removed outlier: 3.582A pdb=" N ALA d1044 " --> pdb=" O SER d1115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'd' and resid 1076 through 1079 Processing sheet with id=AE6, first strand: chain 'd' and resid 1164 through 1167 removed outlier: 4.485A pdb=" N ARG d1164 " --> pdb=" O VAL d1206 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 1271 through 1273 removed outlier: 3.646A pdb=" N ALA d1271 " --> pdb=" O THR e 107 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8672 1.34 - 1.45: 2606 1.45 - 1.57: 14394 1.57 - 1.69: 19 1.69 - 1.81: 165 Bond restraints: 25856 Sorted by residual: bond pdb=" N ILE f 146 " pdb=" CA ILE f 146 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.14e-02 7.69e+03 6.80e+00 bond pdb=" N ILE f 150 " pdb=" CA ILE f 150 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.74e+00 bond pdb=" N GLY e 28 " pdb=" CA GLY e 28 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.14e+00 bond pdb=" N GLN f 148 " pdb=" CA GLN f 148 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.70e+00 bond pdb=" N ARG f 152 " pdb=" CA ARG f 152 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.67e+00 ... (remaining 25851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 33958 1.09 - 2.17: 837 2.17 - 3.26: 163 3.26 - 4.35: 82 4.35 - 5.43: 4 Bond angle restraints: 35044 Sorted by residual: angle pdb=" N ILE d1154 " pdb=" CA ILE d1154 " pdb=" C ILE d1154 " ideal model delta sigma weight residual 111.81 108.41 3.40 8.60e-01 1.35e+00 1.57e+01 angle pdb=" N ILE f 146 " pdb=" CA ILE f 146 " pdb=" C ILE f 146 " ideal model delta sigma weight residual 110.36 106.25 4.11 1.05e+00 9.07e-01 1.53e+01 angle pdb=" CA THR f 151 " pdb=" CB THR f 151 " pdb=" OG1 THR f 151 " ideal model delta sigma weight residual 109.60 104.17 5.43 1.50e+00 4.44e-01 1.31e+01 angle pdb=" CA ILE f 146 " pdb=" C ILE f 146 " pdb=" O ILE f 146 " ideal model delta sigma weight residual 121.27 118.13 3.14 1.04e+00 9.25e-01 9.14e+00 angle pdb=" CA ALA f 149 " pdb=" C ALA f 149 " pdb=" O ALA f 149 " ideal model delta sigma weight residual 120.82 117.74 3.08 1.05e+00 9.07e-01 8.60e+00 ... (remaining 35039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14823 17.95 - 35.90: 826 35.90 - 53.85: 155 53.85 - 71.80: 37 71.80 - 89.75: 5 Dihedral angle restraints: 15846 sinusoidal: 6597 harmonic: 9249 Sorted by residual: dihedral pdb=" CA LYS d1082 " pdb=" C LYS d1082 " pdb=" N ARG d1083 " pdb=" CA ARG d1083 " ideal model delta harmonic sigma weight residual 180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLN d1084 " pdb=" C GLN d1084 " pdb=" N ARG d1085 " pdb=" CA ARG d1085 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ALA c1061 " pdb=" C ALA c1061 " pdb=" N GLN c1062 " pdb=" CA GLN c1062 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 15843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3163 0.043 - 0.086: 526 0.086 - 0.130: 272 0.130 - 0.173: 15 0.173 - 0.216: 1 Chirality restraints: 3977 Sorted by residual: chirality pdb=" CA ILE f 146 " pdb=" N ILE f 146 " pdb=" C ILE f 146 " pdb=" CB ILE f 146 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE f 150 " pdb=" N ILE f 150 " pdb=" C ILE f 150 " pdb=" CB ILE f 150 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE c1112 " pdb=" N ILE c1112 " pdb=" C ILE c1112 " pdb=" CB ILE c1112 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 3974 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG f 152 " 0.477 9.50e-02 1.11e+02 2.14e-01 2.80e+01 pdb=" NE ARG f 152 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG f 152 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG f 152 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG f 152 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP f 145 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C TRP f 145 " -0.038 2.00e-02 2.50e+03 pdb=" O TRP f 145 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE f 146 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER c 546 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO c 547 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO c 547 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO c 547 " -0.026 5.00e-02 4.00e+02 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 219 2.57 - 3.15: 22094 3.15 - 3.74: 37388 3.74 - 4.32: 51387 4.32 - 4.90: 87710 Nonbonded interactions: 198798 Sorted by model distance: nonbonded pdb=" OD1 ASP d 535 " pdb="MG MG d1503 " model vdw 1.988 2.170 nonbonded pdb=" O SER c 182 " pdb=" OH TYR c 186 " model vdw 1.997 3.040 nonbonded pdb=" OD1 ASP d 539 " pdb="MG MG d1503 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR c 354 " pdb=" OE1 GLU c 362 " model vdw 2.102 3.040 nonbonded pdb=" OE2 GLU d 49 " pdb=" OG1 THR d 55 " model vdw 2.132 3.040 ... (remaining 198793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 1 through 152 or resid 159 through 210 or (resid 211 throu \ gh 212 and (name N or name CA or name C or name O )) or resid 213 through 226)) selection = (chain 'b' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 22.860 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25864 Z= 0.123 Angle : 0.469 5.432 35056 Z= 0.253 Chirality : 0.040 0.216 3977 Planarity : 0.005 0.214 4596 Dihedral : 11.779 89.752 9900 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.95 % Allowed : 5.21 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.15), residues: 3217 helix: 1.73 (0.15), residues: 1233 sheet: -1.02 (0.29), residues: 344 loop : -0.50 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d1143 TYR 0.014 0.001 TYR a 168 PHE 0.014 0.001 PHE d 6 TRP 0.009 0.001 TRP d1220 HIS 0.004 0.001 HIS d 505 Details of bonding type rmsd covalent geometry : bond 0.00267 (25856) covalent geometry : angle 0.46527 (35044) hydrogen bonds : bond 0.20742 ( 1108) hydrogen bonds : angle 7.00881 ( 3171) metal coordination : bond 0.00436 ( 8) metal coordination : angle 3.15156 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8351 (p0) REVERT: c 154 MET cc_start: 0.8646 (tpp) cc_final: 0.8065 (tpp) REVERT: c 322 LEU cc_start: 0.8251 (mt) cc_final: 0.7857 (mt) REVERT: c 758 ASP cc_start: 0.8372 (p0) cc_final: 0.8151 (p0) REVERT: d 70 PHE cc_start: 0.7298 (m-80) cc_final: 0.6926 (m-80) REVERT: d 155 MET cc_start: 0.5749 (tmm) cc_final: 0.5073 (tpt) REVERT: d 205 MET cc_start: 0.4380 (mmm) cc_final: 0.3706 (mmm) REVERT: d 233 GLN cc_start: 0.8270 (tt0) cc_final: 0.8069 (mt0) REVERT: d 1112 MET cc_start: 0.6352 (ptm) cc_final: 0.6139 (ppp) REVERT: e 104 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8594 (mp) outliers start: 26 outliers final: 7 residues processed: 328 average time/residue: 0.1682 time to fit residues: 85.9530 Evaluate side-chains 201 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 704 ASP Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain f residue 163 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 443 ASN c1034 HIS c1066 GLN d 103 HIS d 329 GLN d 523 GLN d 552 GLN d 606 HIS d 854 HIS f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.136998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.098453 restraints weight = 45515.430| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.79 r_work: 0.3129 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 25864 Z= 0.272 Angle : 0.683 9.653 35056 Z= 0.349 Chirality : 0.046 0.179 3977 Planarity : 0.005 0.045 4596 Dihedral : 6.973 67.220 3680 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.24 % Allowed : 9.54 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 3217 helix: 1.43 (0.15), residues: 1264 sheet: -0.97 (0.27), residues: 382 loop : -0.72 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d1143 TYR 0.017 0.002 TYR c 731 PHE 0.023 0.002 PHE d1186 TRP 0.012 0.001 TRP d1220 HIS 0.009 0.001 HIS f 60 Details of bonding type rmsd covalent geometry : bond 0.00667 (25856) covalent geometry : angle 0.67810 (35044) hydrogen bonds : bond 0.05372 ( 1108) hydrogen bonds : angle 4.99792 ( 3171) metal coordination : bond 0.01315 ( 8) metal coordination : angle 4.42259 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8546 (p0) REVERT: b 184 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: c 154 MET cc_start: 0.8760 (tpp) cc_final: 0.8395 (tpp) REVERT: c 322 LEU cc_start: 0.8380 (mt) cc_final: 0.8042 (mt) REVERT: c 463 LEU cc_start: 0.8666 (pt) cc_final: 0.8412 (pp) REVERT: c 607 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8071 (mtm) REVERT: c 858 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7937 (pt0) REVERT: c 978 ASP cc_start: 0.8755 (t0) cc_final: 0.8484 (t70) REVERT: c 1009 MET cc_start: 0.8916 (mmt) cc_final: 0.8675 (mmt) REVERT: c 1062 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7588 (mm-40) REVERT: d 70 PHE cc_start: 0.7915 (m-80) cc_final: 0.7444 (m-80) REVERT: d 155 MET cc_start: 0.7027 (tmm) cc_final: 0.5611 (tpt) REVERT: d 205 MET cc_start: 0.5141 (mmm) cc_final: 0.4486 (mtp) REVERT: d 233 GLN cc_start: 0.8353 (tt0) cc_final: 0.7828 (mt0) REVERT: d 787 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: d 1083 ARG cc_start: 0.5566 (mmt180) cc_final: 0.5059 (mmp80) REVERT: d 1112 MET cc_start: 0.7330 (ptm) cc_final: 0.6376 (ppp) REVERT: d 1277 GLU cc_start: 0.8440 (tp30) cc_final: 0.8005 (mt-10) REVERT: e 42 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8236 (mt-10) REVERT: f 25 ASP cc_start: 0.6937 (t0) cc_final: 0.6516 (t0) outliers start: 61 outliers final: 34 residues processed: 253 average time/residue: 0.1475 time to fit residues: 60.3239 Evaluate side-chains 224 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 399 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 443 ASN Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 559 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 658 ILE Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 691 ASP Chi-restraints excluded: chain c residue 789 ILE Chi-restraints excluded: chain c residue 852 VAL Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 847 LEU Chi-restraints excluded: chain d residue 925 LEU Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 166 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 5 GLN c 443 ASN d 505 HIS f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.139169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100094 restraints weight = 45408.547| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.81 r_work: 0.3179 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25864 Z= 0.138 Angle : 0.557 7.680 35056 Z= 0.285 Chirality : 0.042 0.257 3977 Planarity : 0.004 0.038 4596 Dihedral : 6.792 73.881 3676 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 11.38 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.15), residues: 3217 helix: 1.54 (0.15), residues: 1265 sheet: -0.82 (0.28), residues: 359 loop : -0.62 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG d1085 TYR 0.021 0.001 TYR d1062 PHE 0.015 0.001 PHE f 274 TRP 0.013 0.001 TRP c 938 HIS 0.008 0.001 HIS f 252 Details of bonding type rmsd covalent geometry : bond 0.00325 (25856) covalent geometry : angle 0.55341 (35044) hydrogen bonds : bond 0.04358 ( 1108) hydrogen bonds : angle 4.61326 ( 3171) metal coordination : bond 0.00722 ( 8) metal coordination : angle 3.40389 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8387 (p0) REVERT: c 107 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6961 (p90) REVERT: c 154 MET cc_start: 0.8680 (tpp) cc_final: 0.8397 (tpp) REVERT: c 322 LEU cc_start: 0.8260 (mt) cc_final: 0.7982 (mt) REVERT: c 355 MET cc_start: 0.5613 (tmm) cc_final: 0.4875 (tmm) REVERT: c 463 LEU cc_start: 0.8599 (pt) cc_final: 0.8337 (pp) REVERT: c 858 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7922 (pt0) REVERT: c 1062 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7562 (mm-40) REVERT: d 70 PHE cc_start: 0.7917 (m-80) cc_final: 0.7440 (m-80) REVERT: d 155 MET cc_start: 0.7014 (tmm) cc_final: 0.5595 (tpt) REVERT: d 205 MET cc_start: 0.4970 (mmm) cc_final: 0.4353 (mtp) REVERT: d 233 GLN cc_start: 0.8494 (tt0) cc_final: 0.7894 (mt0) REVERT: d 312 MET cc_start: 0.8809 (mmm) cc_final: 0.8330 (mtp) REVERT: d 787 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: d 1083 ARG cc_start: 0.5636 (mmt180) cc_final: 0.5054 (mmp80) REVERT: d 1277 GLU cc_start: 0.8475 (tp30) cc_final: 0.8115 (mt-10) REVERT: e 42 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8218 (mt-10) REVERT: f 25 ASP cc_start: 0.6825 (t0) cc_final: 0.6487 (t0) outliers start: 62 outliers final: 35 residues processed: 257 average time/residue: 0.1457 time to fit residues: 60.3799 Evaluate side-chains 223 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 408 ASP Chi-restraints excluded: chain c residue 443 ASN Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 691 ASP Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 143 MET Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 443 ASN d 606 HIS e 65 ASN f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.139650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100571 restraints weight = 45240.092| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.78 r_work: 0.3188 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25864 Z= 0.126 Angle : 0.532 11.067 35056 Z= 0.273 Chirality : 0.041 0.336 3977 Planarity : 0.004 0.131 4596 Dihedral : 6.706 77.794 3674 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.98 % Allowed : 12.81 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.15), residues: 3217 helix: 1.60 (0.15), residues: 1268 sheet: -0.89 (0.27), residues: 369 loop : -0.56 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG c 925 TYR 0.022 0.001 TYR c 657 PHE 0.014 0.001 PHE d 268 TRP 0.012 0.001 TRP c 938 HIS 0.007 0.001 HIS f 60 Details of bonding type rmsd covalent geometry : bond 0.00293 (25856) covalent geometry : angle 0.52958 (35044) hydrogen bonds : bond 0.03985 ( 1108) hydrogen bonds : angle 4.41868 ( 3171) metal coordination : bond 0.00599 ( 8) metal coordination : angle 2.96216 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8318 (p0) REVERT: c 107 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.6935 (p90) REVERT: c 154 MET cc_start: 0.8675 (tpp) cc_final: 0.8237 (tpp) REVERT: c 322 LEU cc_start: 0.8218 (mt) cc_final: 0.7965 (mt) REVERT: c 463 LEU cc_start: 0.8651 (pt) cc_final: 0.8410 (pp) REVERT: c 470 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8035 (tt) REVERT: c 558 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7302 (ttm-80) REVERT: c 564 LYS cc_start: 0.7879 (tttt) cc_final: 0.7391 (pttm) REVERT: c 607 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7881 (mtm) REVERT: c 858 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7872 (pt0) REVERT: c 982 GLU cc_start: 0.7245 (tp30) cc_final: 0.6883 (tp30) REVERT: c 1062 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7491 (mm-40) REVERT: c 1076 MET cc_start: 0.8723 (mmm) cc_final: 0.8465 (mmm) REVERT: d 70 PHE cc_start: 0.7900 (m-80) cc_final: 0.7440 (m-80) REVERT: d 155 MET cc_start: 0.7007 (tmm) cc_final: 0.5572 (tpt) REVERT: d 205 MET cc_start: 0.4675 (mmm) cc_final: 0.4067 (mtp) REVERT: d 233 GLN cc_start: 0.8502 (tt0) cc_final: 0.8134 (mt0) REVERT: d 787 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: d 1083 ARG cc_start: 0.5539 (mmt180) cc_final: 0.4970 (mmp80) REVERT: d 1112 MET cc_start: 0.7392 (ptm) cc_final: 0.6756 (ppp) REVERT: d 1277 GLU cc_start: 0.8460 (tp30) cc_final: 0.8151 (mt-10) REVERT: f 25 ASP cc_start: 0.6992 (t0) cc_final: 0.6596 (t0) outliers start: 54 outliers final: 29 residues processed: 245 average time/residue: 0.1548 time to fit residues: 62.0040 Evaluate side-chains 219 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 112 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 225 optimal weight: 0.0020 chunk 45 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN d 525 HIS f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101389 restraints weight = 44956.408| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.67 r_work: 0.3204 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25864 Z= 0.110 Angle : 0.511 7.709 35056 Z= 0.262 Chirality : 0.040 0.217 3977 Planarity : 0.004 0.060 4596 Dihedral : 6.641 80.841 3674 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.79 % Allowed : 12.95 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 3217 helix: 1.73 (0.15), residues: 1258 sheet: -0.93 (0.27), residues: 369 loop : -0.51 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 459 TYR 0.014 0.001 TYR d 106 PHE 0.013 0.001 PHE f 274 TRP 0.012 0.001 TRP c 938 HIS 0.012 0.001 HIS f 166 Details of bonding type rmsd covalent geometry : bond 0.00253 (25856) covalent geometry : angle 0.50882 (35044) hydrogen bonds : bond 0.03742 ( 1108) hydrogen bonds : angle 4.27948 ( 3171) metal coordination : bond 0.00488 ( 8) metal coordination : angle 2.61002 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 204 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8287 (p0) REVERT: b 184 GLU cc_start: 0.7907 (mp0) cc_final: 0.7694 (tt0) REVERT: c 107 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.6922 (p90) REVERT: c 154 MET cc_start: 0.8662 (tpp) cc_final: 0.8175 (tpp) REVERT: c 355 MET cc_start: 0.5592 (tmm) cc_final: 0.5343 (tpp) REVERT: c 463 LEU cc_start: 0.8626 (pt) cc_final: 0.8347 (pp) REVERT: c 470 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8032 (tt) REVERT: c 564 LYS cc_start: 0.7768 (tttt) cc_final: 0.7352 (pttm) REVERT: c 607 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7835 (mtm) REVERT: c 858 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7880 (pt0) REVERT: d 39 LEU cc_start: 0.8507 (mp) cc_final: 0.8107 (mt) REVERT: d 70 PHE cc_start: 0.7886 (m-80) cc_final: 0.7250 (m-10) REVERT: d 155 MET cc_start: 0.6968 (tmm) cc_final: 0.5583 (tpt) REVERT: d 205 MET cc_start: 0.4650 (mmm) cc_final: 0.4009 (mtp) REVERT: d 233 GLN cc_start: 0.8555 (tt0) cc_final: 0.7914 (mt0) REVERT: d 312 MET cc_start: 0.8790 (mmm) cc_final: 0.8578 (mtp) REVERT: d 787 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: d 1083 ARG cc_start: 0.5508 (mmt180) cc_final: 0.5088 (mmp80) REVERT: d 1112 MET cc_start: 0.7341 (ptm) cc_final: 0.6736 (ptm) REVERT: d 1277 GLU cc_start: 0.8429 (tp30) cc_final: 0.8222 (mt-10) REVERT: f 25 ASP cc_start: 0.6669 (t0) cc_final: 0.6331 (t0) outliers start: 76 outliers final: 45 residues processed: 260 average time/residue: 0.1411 time to fit residues: 60.3811 Evaluate side-chains 234 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 342 ILE Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 443 ASN Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 691 ASP Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain c residue 1031 MET Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 143 MET Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 646 ILE Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 113 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 300 optimal weight: 0.9980 chunk 278 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN d 606 HIS f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.144301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104841 restraints weight = 45560.844| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.86 r_work: 0.3179 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25864 Z= 0.131 Angle : 0.517 7.175 35056 Z= 0.265 Chirality : 0.041 0.144 3977 Planarity : 0.004 0.043 4596 Dihedral : 6.620 81.943 3674 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.57 % Allowed : 14.02 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.15), residues: 3217 helix: 1.75 (0.15), residues: 1262 sheet: -0.87 (0.27), residues: 366 loop : -0.48 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 762 TYR 0.023 0.001 TYR c 657 PHE 0.013 0.001 PHE d 268 TRP 0.011 0.001 TRP c 938 HIS 0.015 0.001 HIS f 60 Details of bonding type rmsd covalent geometry : bond 0.00311 (25856) covalent geometry : angle 0.51461 (35044) hydrogen bonds : bond 0.03787 ( 1108) hydrogen bonds : angle 4.24126 ( 3171) metal coordination : bond 0.00609 ( 8) metal coordination : angle 2.60965 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 194 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8305 (p0) REVERT: c 107 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.6941 (p90) REVERT: c 154 MET cc_start: 0.8684 (tpp) cc_final: 0.8392 (tpp) REVERT: c 211 TRP cc_start: 0.7260 (m-10) cc_final: 0.6996 (m-10) REVERT: c 355 MET cc_start: 0.6055 (tmm) cc_final: 0.5826 (tmm) REVERT: c 463 LEU cc_start: 0.8649 (pt) cc_final: 0.8377 (pp) REVERT: c 470 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8041 (tt) REVERT: c 558 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7528 (mmm-85) REVERT: c 564 LYS cc_start: 0.7703 (tttt) cc_final: 0.7281 (pttm) REVERT: c 607 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7911 (mtm) REVERT: c 858 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7902 (pt0) REVERT: c 982 GLU cc_start: 0.7239 (tp30) cc_final: 0.6894 (tp30) REVERT: d 39 LEU cc_start: 0.8566 (mp) cc_final: 0.8191 (mt) REVERT: d 70 PHE cc_start: 0.7899 (m-80) cc_final: 0.7297 (m-10) REVERT: d 155 MET cc_start: 0.7028 (tmm) cc_final: 0.5530 (tpt) REVERT: d 205 MET cc_start: 0.4702 (mmm) cc_final: 0.4080 (mtp) REVERT: d 233 GLN cc_start: 0.8551 (tt0) cc_final: 0.7897 (mt0) REVERT: d 312 MET cc_start: 0.8819 (mmm) cc_final: 0.8606 (mtp) REVERT: d 400 LYS cc_start: 0.8216 (tttt) cc_final: 0.7879 (ttmt) REVERT: d 787 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: d 1083 ARG cc_start: 0.5512 (mmt180) cc_final: 0.4975 (mmp80) REVERT: d 1112 MET cc_start: 0.7346 (ptm) cc_final: 0.6773 (ptm) REVERT: d 1277 GLU cc_start: 0.8490 (tp30) cc_final: 0.8213 (mt-10) REVERT: e 88 GLN cc_start: 0.7542 (tp-100) cc_final: 0.7126 (tp40) REVERT: f 25 ASP cc_start: 0.6654 (t0) cc_final: 0.6273 (t0) outliers start: 70 outliers final: 45 residues processed: 247 average time/residue: 0.1332 time to fit residues: 55.1711 Evaluate side-chains 235 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 342 ILE Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 143 MET Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 633 ILE Chi-restraints excluded: chain d residue 646 ILE Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 909 THR Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain d residue 1215 LEU Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 154 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN d 606 HIS d1190 ASN f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.138951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100959 restraints weight = 45496.215| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.87 r_work: 0.3141 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25864 Z= 0.189 Angle : 0.559 7.225 35056 Z= 0.287 Chirality : 0.042 0.146 3977 Planarity : 0.004 0.040 4596 Dihedral : 6.716 81.091 3673 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.79 % Allowed : 14.53 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3217 helix: 1.62 (0.15), residues: 1271 sheet: -0.86 (0.27), residues: 376 loop : -0.58 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 762 TYR 0.027 0.001 TYR c 657 PHE 0.013 0.001 PHE d 512 TRP 0.011 0.001 TRP c 938 HIS 0.010 0.001 HIS f 60 Details of bonding type rmsd covalent geometry : bond 0.00461 (25856) covalent geometry : angle 0.55642 (35044) hydrogen bonds : bond 0.04185 ( 1108) hydrogen bonds : angle 4.32397 ( 3171) metal coordination : bond 0.00917 ( 8) metal coordination : angle 2.88741 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 190 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8354 (p0) REVERT: c 154 MET cc_start: 0.8785 (tpp) cc_final: 0.8430 (tpp) REVERT: c 355 MET cc_start: 0.6135 (tmm) cc_final: 0.5883 (tmm) REVERT: c 463 LEU cc_start: 0.8651 (pt) cc_final: 0.8366 (pp) REVERT: c 470 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8025 (tt) REVERT: c 558 ARG cc_start: 0.7751 (mtp85) cc_final: 0.7498 (mmm-85) REVERT: c 564 LYS cc_start: 0.7687 (tttt) cc_final: 0.7259 (pttm) REVERT: c 607 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.7974 (mtm) REVERT: c 858 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7926 (pt0) REVERT: d 70 PHE cc_start: 0.7976 (m-80) cc_final: 0.7520 (m-80) REVERT: d 155 MET cc_start: 0.6909 (tmm) cc_final: 0.5576 (tpt) REVERT: d 205 MET cc_start: 0.4724 (mmm) cc_final: 0.4106 (mtp) REVERT: d 233 GLN cc_start: 0.8574 (tt0) cc_final: 0.7915 (mt0) REVERT: d 400 LYS cc_start: 0.8185 (tttt) cc_final: 0.7870 (ttmt) REVERT: d 787 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: d 1083 ARG cc_start: 0.5624 (mmt180) cc_final: 0.5057 (mmp80) REVERT: d 1112 MET cc_start: 0.7415 (ptm) cc_final: 0.6864 (ptm) REVERT: d 1192 ARG cc_start: 0.7323 (tmt170) cc_final: 0.7082 (tmm-80) REVERT: d 1277 GLU cc_start: 0.8490 (tp30) cc_final: 0.8210 (mt-10) REVERT: f 25 ASP cc_start: 0.6690 (t0) cc_final: 0.6348 (t0) outliers start: 76 outliers final: 51 residues processed: 251 average time/residue: 0.1477 time to fit residues: 61.1724 Evaluate side-chains 238 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 443 ASN Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 500 LEU Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 909 THR Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain d residue 1190 ASN Chi-restraints excluded: chain d residue 1215 LEU Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 161 ILE Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 9 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 319 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN d1239 ASN e 88 GLN f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.137814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098701 restraints weight = 44899.103| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.68 r_work: 0.3158 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25864 Z= 0.167 Angle : 0.549 7.367 35056 Z= 0.281 Chirality : 0.041 0.155 3977 Planarity : 0.004 0.042 4596 Dihedral : 6.695 81.391 3673 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.50 % Allowed : 15.41 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 3217 helix: 1.61 (0.15), residues: 1270 sheet: -0.85 (0.27), residues: 376 loop : -0.58 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 295 TYR 0.028 0.001 TYR d1062 PHE 0.017 0.001 PHE c 214 TRP 0.012 0.001 TRP c 938 HIS 0.018 0.001 HIS f 60 Details of bonding type rmsd covalent geometry : bond 0.00405 (25856) covalent geometry : angle 0.54719 (35044) hydrogen bonds : bond 0.04035 ( 1108) hydrogen bonds : angle 4.29789 ( 3171) metal coordination : bond 0.00836 ( 8) metal coordination : angle 2.75894 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8311 (p0) REVERT: c 154 MET cc_start: 0.8756 (tpp) cc_final: 0.8440 (tpp) REVERT: c 355 MET cc_start: 0.6179 (tmm) cc_final: 0.5956 (tmm) REVERT: c 463 LEU cc_start: 0.8636 (pt) cc_final: 0.8357 (pp) REVERT: c 470 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8023 (tt) REVERT: c 558 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7542 (mmm-85) REVERT: c 564 LYS cc_start: 0.7654 (tttt) cc_final: 0.7242 (pttm) REVERT: c 607 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7933 (mtm) REVERT: c 858 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7924 (pt0) REVERT: d 70 PHE cc_start: 0.7967 (m-80) cc_final: 0.7492 (m-80) REVERT: d 155 MET cc_start: 0.6988 (tmm) cc_final: 0.5587 (tpt) REVERT: d 205 MET cc_start: 0.4696 (mmm) cc_final: 0.4065 (mtp) REVERT: d 233 GLN cc_start: 0.8569 (tt0) cc_final: 0.7863 (mt0) REVERT: d 400 LYS cc_start: 0.8109 (tttt) cc_final: 0.7815 (ttmt) REVERT: d 787 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: d 1083 ARG cc_start: 0.5633 (mmt180) cc_final: 0.5040 (mmp80) REVERT: d 1112 MET cc_start: 0.7391 (ptm) cc_final: 0.6854 (ptm) REVERT: d 1277 GLU cc_start: 0.8481 (tp30) cc_final: 0.8231 (mt-10) REVERT: f 25 ASP cc_start: 0.6761 (t0) cc_final: 0.6423 (t70) outliers start: 68 outliers final: 52 residues processed: 240 average time/residue: 0.1372 time to fit residues: 55.3176 Evaluate side-chains 234 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 433 THR Chi-restraints excluded: chain c residue 443 ASN Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 691 ASP Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain c residue 865 VAL Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 909 THR Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1098 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain d residue 1215 LEU Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 161 ILE Chi-restraints excluded: chain f residue 163 LEU Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 120 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 252 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 269 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 349 HIS c 443 ASN d1190 ASN ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.141150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101909 restraints weight = 45677.731| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.93 r_work: 0.3106 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25864 Z= 0.221 Angle : 0.598 7.918 35056 Z= 0.305 Chirality : 0.043 0.187 3977 Planarity : 0.004 0.048 4596 Dihedral : 6.794 80.445 3673 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.75 % Allowed : 15.08 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 3217 helix: 1.47 (0.15), residues: 1276 sheet: -0.88 (0.28), residues: 368 loop : -0.67 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d1087 TYR 0.029 0.001 TYR c 657 PHE 0.015 0.002 PHE c 214 TRP 0.010 0.001 TRP c 938 HIS 0.010 0.001 HIS f 252 Details of bonding type rmsd covalent geometry : bond 0.00542 (25856) covalent geometry : angle 0.59502 (35044) hydrogen bonds : bond 0.04389 ( 1108) hydrogen bonds : angle 4.40177 ( 3171) metal coordination : bond 0.01110 ( 8) metal coordination : angle 3.06210 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 185 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8251 (p0) REVERT: c 154 MET cc_start: 0.8774 (tpp) cc_final: 0.8405 (tpp) REVERT: c 355 MET cc_start: 0.6260 (tmm) cc_final: 0.6027 (tmm) REVERT: c 463 LEU cc_start: 0.8633 (pt) cc_final: 0.8394 (pp) REVERT: c 470 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8051 (tt) REVERT: c 558 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7459 (mmt-90) REVERT: c 564 LYS cc_start: 0.7793 (tttt) cc_final: 0.7428 (pttm) REVERT: c 607 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7811 (mtm) REVERT: c 858 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7846 (pt0) REVERT: d 70 PHE cc_start: 0.8016 (m-80) cc_final: 0.7363 (m-10) REVERT: d 155 MET cc_start: 0.6994 (tmm) cc_final: 0.5614 (tpt) REVERT: d 205 MET cc_start: 0.4758 (mmm) cc_final: 0.4171 (mtp) REVERT: d 233 GLN cc_start: 0.8602 (tt0) cc_final: 0.8318 (mt0) REVERT: d 400 LYS cc_start: 0.7963 (tttt) cc_final: 0.7688 (ttmt) REVERT: d 787 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: d 1083 ARG cc_start: 0.5618 (mmt180) cc_final: 0.4997 (mmp80) REVERT: d 1112 MET cc_start: 0.7324 (ptm) cc_final: 0.6798 (ptm) REVERT: e 42 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8226 (mt-10) REVERT: f 25 ASP cc_start: 0.6875 (t0) cc_final: 0.6541 (t70) outliers start: 75 outliers final: 52 residues processed: 249 average time/residue: 0.1482 time to fit residues: 61.4760 Evaluate side-chains 233 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 433 THR Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 691 ASP Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain c residue 865 VAL Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 317 VAL Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 860 LEU Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 909 THR Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1098 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 161 ILE Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 263 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 227 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN e 88 GLN f 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.137514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099736 restraints weight = 45685.738| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.90 r_work: 0.3116 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25864 Z= 0.221 Angle : 0.598 7.826 35056 Z= 0.307 Chirality : 0.043 0.163 3977 Planarity : 0.004 0.076 4596 Dihedral : 6.787 80.254 3671 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.35 % Allowed : 15.41 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 3217 helix: 1.42 (0.15), residues: 1278 sheet: -0.97 (0.27), residues: 376 loop : -0.74 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG d 295 TYR 0.027 0.002 TYR c 657 PHE 0.014 0.001 PHE c 214 TRP 0.012 0.001 TRP c 938 HIS 0.011 0.001 HIS f 60 Details of bonding type rmsd covalent geometry : bond 0.00542 (25856) covalent geometry : angle 0.59553 (35044) hydrogen bonds : bond 0.04359 ( 1108) hydrogen bonds : angle 4.41353 ( 3171) metal coordination : bond 0.01125 ( 8) metal coordination : angle 3.06553 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8361 (p0) REVERT: c 154 MET cc_start: 0.8818 (tpp) cc_final: 0.8485 (tpp) REVERT: c 355 MET cc_start: 0.6232 (tmm) cc_final: 0.5977 (tmm) REVERT: c 463 LEU cc_start: 0.8638 (pt) cc_final: 0.8363 (pp) REVERT: c 470 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8021 (tt) REVERT: c 558 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7367 (mmt-90) REVERT: c 564 LYS cc_start: 0.7692 (tttt) cc_final: 0.7259 (pttm) REVERT: c 607 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: c 858 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7865 (pt0) REVERT: d 70 PHE cc_start: 0.8158 (m-80) cc_final: 0.7449 (m-10) REVERT: d 155 MET cc_start: 0.7069 (tmm) cc_final: 0.5610 (tpt) REVERT: d 205 MET cc_start: 0.4756 (mmm) cc_final: 0.4152 (mtp) REVERT: d 233 GLN cc_start: 0.8670 (tt0) cc_final: 0.8367 (mt0) REVERT: d 296 LEU cc_start: 0.7611 (tt) cc_final: 0.7038 (tp) REVERT: d 376 GLU cc_start: 0.8351 (tp30) cc_final: 0.8136 (tm-30) REVERT: d 400 LYS cc_start: 0.8157 (tttt) cc_final: 0.7922 (ttmt) REVERT: d 787 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7321 (mp10) REVERT: d 1112 MET cc_start: 0.7415 (ptm) cc_final: 0.6916 (ptm) REVERT: d 1185 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7926 (tp30) REVERT: e 42 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8464 (mt-10) REVERT: f 25 ASP cc_start: 0.7038 (t0) cc_final: 0.6779 (t0) outliers start: 64 outliers final: 54 residues processed: 233 average time/residue: 0.1404 time to fit residues: 54.2992 Evaluate side-chains 229 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 365 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 433 THR Chi-restraints excluded: chain c residue 470 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 500 LEU Chi-restraints excluded: chain c residue 501 SER Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 607 MET Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 691 ASP Chi-restraints excluded: chain c residue 762 THR Chi-restraints excluded: chain c residue 865 VAL Chi-restraints excluded: chain d residue 78 CYS Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 317 VAL Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 787 GLN Chi-restraints excluded: chain d residue 793 TYR Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 880 VAL Chi-restraints excluded: chain d residue 909 THR Chi-restraints excluded: chain d residue 1024 ILE Chi-restraints excluded: chain d residue 1033 GLU Chi-restraints excluded: chain d residue 1053 VAL Chi-restraints excluded: chain d residue 1098 VAL Chi-restraints excluded: chain d residue 1104 HIS Chi-restraints excluded: chain d residue 1132 ILE Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 60 HIS Chi-restraints excluded: chain f residue 161 ILE Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 237 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 230 optimal weight: 0.0060 chunk 43 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 188 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 5 GLN b 61 HIS c 443 ASN f 60 HIS ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.138215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099086 restraints weight = 44872.002| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.66 r_work: 0.3175 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25864 Z= 0.125 Angle : 0.543 13.864 35056 Z= 0.277 Chirality : 0.041 0.172 3977 Planarity : 0.004 0.060 4596 Dihedral : 6.669 82.186 3671 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.20 % Allowed : 15.56 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.15), residues: 3217 helix: 1.61 (0.15), residues: 1269 sheet: -0.89 (0.28), residues: 368 loop : -0.61 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG d 295 TYR 0.025 0.001 TYR c 657 PHE 0.014 0.001 PHE d 673 TRP 0.016 0.001 TRP c 938 HIS 0.004 0.001 HIS f 60 Details of bonding type rmsd covalent geometry : bond 0.00292 (25856) covalent geometry : angle 0.54076 (35044) hydrogen bonds : bond 0.03839 ( 1108) hydrogen bonds : angle 4.27100 ( 3171) metal coordination : bond 0.00624 ( 8) metal coordination : angle 2.70371 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6624.43 seconds wall clock time: 113 minutes 38.95 seconds (6818.95 seconds total)